We investigate the hydrodynamic boundary condition for simple nanofluidic systems such as argon and methane flowing in graphene nanochannels using equilibrium molecular dynamics simulations (EMD) in conjunction with our recently proposed method [J. S. Hansen, B. D. Todd, and P. J. Daivis, Phys. Rev. E 84, 016313 (2011)]. We first calculate the fluid-graphene interfacial friction coefficient, from which we can predict the slip length and the average velocity of the first fluid layer close to the wall (referred to as the slip velocity). Using direct nonequilibrium molecular dynamics simulations (NEMD) we then calculate the slip length and slip velocity from the streaming velocity profiles in Poiseuille and Couette flows. The slip lengths and slip velocities from the NEMD simulations are found to be in excellent agreement with our EMD predictions. Our EMD method therefore enables one to directly calculate this intrinsic friction coefficient between fluid and solid and the slip length for a given fluid and solid, which is otherwise tedious to calculate using direct NEMD simulations at low pressure gradients or shear rates. The advantages of the EMD method over the NEMD method to calculate the slip lengths/flow rates for nanofluidic systems are discussed, and we finally examine the dynamic behaviour of slip due to an externally applied field and shear rate.